# Community

**URL:** https://discourse.slicer.org/c/community/12.md?no_subcategories=false&page=26

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

**Page:** 27

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## [vmtkcenterlines openprofiles issue](https://discourse.slicer.org/t/vmtkcenterlines-openprofiles-issue/21906)

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**Author:** [@hemjo](https://discourse.slicer.org/u/hemjo)\
**Replies:** 5\
**Last updated:** [February 12, 2022, 5:28am UTC](https://discourse.slicer.org/t/vmtkcenterlines-openprofiles-issue/21906 "2022-02-12T05:28:12Z")

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I am trying to use vmtkcenterlines, but even on the test data aorta-surface-open-ends.stl when I run vmtksurfacereader -ifile aorta-surface-open-ends.stl --pipe vmtkcenterlines -seedselector openprofiles -endpoints 1 -o…

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## [No module named vtkmodules.vtkCommonCore](https://discourse.slicer.org/t/no-module-named-vtkmodules-vtkcommoncore/21854)

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**Author:** [@n\_h](https://discourse.slicer.org/u/n_h)\
**Replies:** 7\
**Last updated:** [February 9, 2022, 11:43am UTC](https://discourse.slicer.org/t/no-module-named-vtkmodules-vtkcommoncore/21854 "2022-02-09T11:43:13Z")

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Hey, I have recently got in touch with vmtk but I have still some issues making it work from python scripts. I would like to used it to implement an automatic segmentation and meshing workflow. I have set up an Ubuntu …

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## [2022.02.08 Weekly Meeting](https://discourse.slicer.org/t/2022-02-08-weekly-meeting/21843)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [February 7, 2022, 7:12pm UTC](https://discourse.slicer.org/t/2022-02-08-weekly-meeting/21843 "2022-02-07T19:12:48Z")

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Tomorrow, we will be having our next weekly hangout at 10:00 AM ET until 11 PM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress Please po…

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## [Can I use lmaps generated from CIP to extract features with Pyradiomics?](https://discourse.slicer.org/t/can-i-use-lmaps-generated-from-cip-to-extract-features-with-pyradiomics/21785)

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**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 0\
**Last updated:** [February 3, 2022, 5:19pm UTC](https://discourse.slicer.org/t/can-i-use-lmaps-generated-from-cip-to-extract-features-with-pyradiomics/21785 "2022-02-03T17:19:48Z")

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I am new to pyradiomics. I have used CIPs Interactive lobe segmentation to get a lung label map(lmap.nrrd). and I’m using a ct.nrrd as my input volume, obtained from dicoms. I wanted to know if I can use this ct and lma…

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## [2022.02.01 Weekly Meeting](https://discourse.slicer.org/t/2022-02-01-weekly-meeting/21720)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 2\
**Last updated:** [February 1, 2022, 12:55pm UTC](https://discourse.slicer.org/t/2022-02-01-weekly-meeting/21720 "2022-02-01T12:55:16Z")

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Tomorrow, we will be having our next weekly hangout at 10:00 AM ET until 11 PM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress Custom MR…

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## [Brief Introduction. Help needed](https://discourse.slicer.org/t/brief-introduction-help-needed/21680)

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**Author:** [@dnevado](https://discourse.slicer.org/u/dnevado)\
**Replies:** 0\
**Last updated:** [January 28, 2022, 2:56pm UTC](https://discourse.slicer.org/t/brief-introduction-help-needed/21680 "2022-01-28T14:56:21Z")

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First, pleasure to be part of this discussion group. I am a newbie on this topic and struggling how to address on of the research someone has requested me to have a look. Objective is to analyze the likely progression of…

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## [Slicer radiomics-features](https://discourse.slicer.org/t/slicer-radiomics-features/21280)

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**Author:** [@MPhilip](https://discourse.slicer.org/u/MPhilip)\
**Replies:** 16\
**Last updated:** [January 28, 2022, 12:25pm UTC](https://discourse.slicer.org/t/slicer-radiomics-features/21280 "2022-01-28T12:25:17Z")

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Operating system:Windows 10 enterprise Slicer version:3D slicer 4.13.0-2021-12-15 Hi I was extracting features using the Slicer radiomics module from GTV of RTStruct. But when I see the table containing the features m…

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## [2022.01.25 Weekly Meeting](https://discourse.slicer.org/t/2022-01-25-weekly-meeting/21603)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [January 25, 2022, 11:40am UTC](https://discourse.slicer.org/t/2022-01-25-weekly-meeting/21603 "2022-01-25T11:40:24Z")

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Tomorrow we will be having our next weekly hangout at 10:00 AM ET until 11 PM ET. Anyone is welcome to join to ask questions at https://bit.ly/slicer-googlemeet-hosted-by-kitware Agenda: Slicer 5 progress Please pos…

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## [Radiomic features with identical values](https://discourse.slicer.org/t/radiomic-features-with-identical-values/18188)

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**Author:** [@Gergely\_Orsi](https://discourse.slicer.org/u/Gergely_Orsi)\
**Replies:** 3\
**Last updated:** [January 21, 2022, 10:21am UTC](https://discourse.slicer.org/t/radiomic-features-with-identical-values/18188 "2022-01-21T10:21:33Z")

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Dear Community Members, I do not have too much prior experience with pyradiomics, so sorry for the dull question. I have several features with identical values and I’d like to know if it’s ok, or not. Examples: In Gr…

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## [How radiomics calculate numbers](https://discourse.slicer.org/t/how-radiomics-calculate-numbers/19391)

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**Author:** [@hotsen](https://discourse.slicer.org/u/hotsen)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 10:20am UTC](https://discourse.slicer.org/t/how-radiomics-calculate-numbers/19391 "2022-01-21T10:20:19Z")

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Hi all, I got some basic questions about radiomics. Say I have input image A and a lablemap B as input region, I got first-order features like mean, min, max using Radiomics. I assume Radiomics first generate an array u…

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## [Image type input to pyRadiommics](https://discourse.slicer.org/t/image-type-input-to-pyradiommics/17893)

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**Author:** [@11117](https://discourse.slicer.org/u/11117)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 10:07am UTC](https://discourse.slicer.org/t/image-type-input-to-pyradiommics/17893 "2022-01-21T10:07:49Z")

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Hi, pyRadiommics knows how to handle float input? (nrrd file with float arrays) or it will convert it to int? or there is a any problem with very high float variable? Tnx

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## [Feature Extraction](https://discourse.slicer.org/t/feature-extraction/17706)

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**Author:** [@HAFSA](https://discourse.slicer.org/u/HAFSA)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 10:05am UTC](https://discourse.slicer.org/t/feature-extraction/17706 "2022-01-21T10:05:04Z")

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Hey: I want to extract the radiomic features of 2D Slices. But it fails when the mask with only background is found or no tumor area. You can say blank slices .On the other hand I want to extract the feature of all slic…

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## [Help in deep understanding pyRadiomics](https://discourse.slicer.org/t/help-in-deep-understanding-pyradiomics/16269)

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**Author:** [@11117](https://discourse.slicer.org/u/11117)\
**Replies:** 3\
**Last updated:** [January 21, 2022, 10:01am UTC](https://discourse.slicer.org/t/help-in-deep-understanding-pyradiomics/16269 "2022-01-21T10:01:12Z")

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Hello everyone, I’m trying to understand my results that I get from pyradiomics - FeatureExtractor and I have two questions: I want to understand what values the extractor gets me, so I calculate manually the energy, …

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## [vmtkcenterlinegeometry - can't view output file](https://discourse.slicer.org/t/vmtkcenterlinegeometry-cant-view-output-file/21544)

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**Author:** [@fsneden](https://discourse.slicer.org/u/fsneden)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 9:19am UTC](https://discourse.slicer.org/t/vmtkcenterlinegeometry-cant-view-output-file/21544 "2022-01-21T09:19:39Z")

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Hi, Have used vmtkcenterline geometry to calculate tortuousity of a carotid artery. Output runs fine; the file is written under .vtp extension as in tutorial. However, I want numbers that relate to tortuousity, curvatur…

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## [Segmented or unsegmented head RGBA volume datasets](https://discourse.slicer.org/t/segmented-or-unsegmented-head-rgba-volume-datasets/21541)

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**Author:** [@davide445](https://discourse.slicer.org/u/davide445)\
**Replies:** 0\
**Last updated:** [January 20, 2022, 6:54am UTC](https://discourse.slicer.org/t/segmented-or-unsegmented-head-rgba-volume-datasets/21541 "2022-01-20T06:54:33Z")

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Not sure this is the right section to ask, anyway my question it’s not related to Slicer usage. Looking at these examples wanted to ask if someone know or has an idea where to search for other RGBA or anyway colored v…

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## [MSc Project using 3dSlicer Registration of Brain Scans](https://discourse.slicer.org/t/msc-project-using-3dslicer-registration-of-brain-scans/21532)

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**Author:** [@sandigeeup](https://discourse.slicer.org/u/sandigeeup)\
**Replies:** 0\
**Last updated:** [January 19, 2022, 9:31pm UTC](https://discourse.slicer.org/t/msc-project-using-3dslicer-registration-of-brain-scans/21532 "2022-01-19T21:31:17Z")

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Just undertaken a project for my MSc in Medical Visualisation at Glasgow University. I had to register and render three datasets of a brain tumour using MRI, CT and PET. It was no easy feat given I am a complete newbie t…

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## [Extract multiple labels from one image without reloading image and mask data? ](https://discourse.slicer.org/t/extract-multiple-labels-from-one-image-without-reloading-image-and-mask-data/21468)

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**Author:** [@Sebastian\_Nagel](https://discourse.slicer.org/u/Sebastian_Nagel)\
**Replies:** 3\
**Last updated:** [January 19, 2022, 8:40pm UTC](https://discourse.slicer.org/t/extract-multiple-labels-from-one-image-without-reloading-image-and-mask-data/21468 "2022-01-19T20:40:17Z")

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Dear Community, we performed a CT segmentation for which we placed multiple labels into one dataset. Now when we start extracting the features using either the command line or a Jupyter notebook, the image and mask dat…

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## [Radiomics warning Size in specified 2D dimension (0) is greater than 1, cannot calculate 2D shape](https://discourse.slicer.org/t/radiomics-warning-size-in-specified-2d-dimension-0-is-greater-than-1-cannot-calculate-2d-shape/21424)

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**Author:** [@zandarina](https://discourse.slicer.org/u/zandarina)\
**Replies:** 2\
**Last updated:** [January 18, 2022, 12:38pm UTC](https://discourse.slicer.org/t/radiomics-warning-size-in-specified-2d-dimension-0-is-greater-than-1-cannot-calculate-2d-shape/21424 "2022-01-18T12:38:39Z")

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Dear all, I am trying to compute the radiomics and I get this warning: Size in specified 2D dimension (0) is greater than 1, cannot calculate 2D shape result = extractor.execute(image, mask) and the image size is: (…

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## [Pyradiomics (GLCM) calculation](https://discourse.slicer.org/t/pyradiomics-glcm-calculation/21154)

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**Author:** [@tenzin\_kunkyab](https://discourse.slicer.org/u/tenzin_kunkyab)\
**Replies:** 2\
**Last updated:** [January 14, 2022, 7:34pm UTC](https://discourse.slicer.org/t/pyradiomics-glcm-calculation/21154 "2022-01-14T19:34:47Z")

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Hi developers, I am working on implementing a past study on radiomics. The extract from the published report includes the definition of the GLCM radiomic features as follows in their matlab software: “Neighbouring voxe…

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## [add flow extension to irregularly shaped outlet](https://discourse.slicer.org/t/add-flow-extension-to-irregularly-shaped-outlet/21445)

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**Author:** [@susk](https://discourse.slicer.org/u/susk)\
**Replies:** 0\
**Last updated:** [January 13, 2022, 1:58pm UTC](https://discourse.slicer.org/t/add-flow-extension-to-irregularly-shaped-outlet/21445 "2022-01-13T13:58:34Z")

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I am trying to add a flow extension to an outlet using vmtkflowextensions. However, the outlet has a very irregular shape due to the presence of plaque, and the added flow extension does not fit the outlet very well: …

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## [Feature extraction from anisotropic 3D VOIs: should we apply Force2D potion?](https://discourse.slicer.org/t/feature-extraction-from-anisotropic-3d-vois-should-we-apply-force2d-potion/21285)

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**Author:** [@Eugene](https://discourse.slicer.org/u/Eugene)\
**Replies:** 5\
**Last updated:** [January 12, 2022, 2:03am UTC](https://discourse.slicer.org/t/feature-extraction-from-anisotropic-3d-vois-should-we-apply-force2d-potion/21285 "2022-01-12T02:03:54Z")

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Greetings expert team. Much obliged for your great invention and maintanance of pyradiomics! I’m currently working on some MRI T2WI data, consecutively delineating 2D ROIs in each slice on the coronal plane. I noticed t…

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## [Pyradiomics LoG filter voxel or physical space?](https://discourse.slicer.org/t/pyradiomics-log-filter-voxel-or-physical-space/19944)

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**Author:** [@GVK](https://discourse.slicer.org/u/GVK)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 12:20pm UTC](https://discourse.slicer.org/t/pyradiomics-log-filter-voxel-or-physical-space/19944 "2022-01-11T12:20:52Z")

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Operating system:na Slicer version:na Expected behavior:na Actual behavior:na In pyradiomics default settings, are the settings of the LoG filter defined in voxel space or in physical space?

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## [Intensity Resampling in SlicerRadiomicc](https://discourse.slicer.org/t/intensity-resampling-in-slicerradiomicc/17134)

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**Author:** [@Giada\_Fiore](https://discourse.slicer.org/u/Giada_Fiore)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 12:14pm UTC](https://discourse.slicer.org/t/intensity-resampling-in-slicerradiomicc/17134 "2022-01-11T12:14:28Z")

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Hi, I’m working with CT images in Slicer Radiomics, but I have a doubt: is intensity resampling absolute or relative to ROI? I have set a fixed bin length. Thank you!

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## [Classification of features radiomics](https://discourse.slicer.org/t/classification-of-features-radiomics/17077)

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**Author:** [@Tonyale1975](https://discourse.slicer.org/u/Tonyale1975)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 12:09pm UTC](https://discourse.slicer.org/t/classification-of-features-radiomics/17077 "2022-01-11T12:09:06Z")

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Dear PyRadiomics / 3DSlicer community, I have been extracting radiomic features with PyRadiomics. But, when I try to carry out a classification using machine learning techniques, usually the different classifiers class…

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## [Syntax parameter file](https://discourse.slicer.org/t/syntax-parameter-file/16907)

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**Author:** [@Marion](https://discourse.slicer.org/u/Marion)\
**Replies:** 6\
**Last updated:** [January 11, 2022, 12:06pm UTC](https://discourse.slicer.org/t/syntax-parameter-file/16907 "2022-01-11T12:06:02Z")

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Operating system: macOS High Sierra (10.13.6) Slicer version: 4.11.20200930 Expected behavior: Actual behavior: Hi everyone, I have a problem with the syntax of the parameter file for the Radiomics module. I attach …

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## [number of extracted features](https://discourse.slicer.org/t/number-of-extracted-features/21002)

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**Author:** [@mina](https://discourse.slicer.org/u/mina)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 11:32am UTC](https://discourse.slicer.org/t/number-of-extracted-features/21002 "2022-01-11T11:32:14Z")

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Operating system:IOS Slicer version:.11.20210226 r29738 hello, I have a question about the extracted features by Radiomics extension. when I resample a MRI sequence, for some sapcing -dimensions it extracts 140 featu…

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## [Changing pyradiomics json Params file](https://discourse.slicer.org/t/changing-pyradiomics-json-params-file/21075)

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**Author:** [@Valentina\_Nepi](https://discourse.slicer.org/u/Valentina_Nepi)\
**Replies:** 3\
**Last updated:** [January 11, 2022, 11:31am UTC](https://discourse.slicer.org/t/changing-pyradiomics-json-params-file/21075 "2022-01-11T11:31:29Z")

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Is it possible to change this file? I’ve tried to use a params file.yaml converted in json but it doesn’t work. Any suggestions? Thanks

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## [2022.01.11 Weekly Meeting](https://discourse.slicer.org/t/2022-01-11-weekly-meeting/21397)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 11:19am UTC](https://discourse.slicer.org/t/2022-01-11-weekly-meeting/21397 "2022-01-11T11:19:50Z")

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Next Tuesday, we will be having our next weekly hangout at 11:00 AM ET until 12 PM ET, immediately after the Project Week meeting. We will be using the same Zoom link as the project week meeting. Anyone is welcome to j…

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## [Pyradiomics in 3D Slicer - install via Extension Manager?](https://discourse.slicer.org/t/pyradiomics-in-3d-slicer-install-via-extension-manager/21394)

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**Author:** [@Gordon\_Cowell](https://discourse.slicer.org/u/Gordon_Cowell)\
**Replies:** 2\
**Last updated:** [January 11, 2022, 1:07am UTC](https://discourse.slicer.org/t/pyradiomics-in-3d-slicer-install-via-extension-manager/21394 "2022-01-11T01:07:43Z")

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Hi, I’m needing to switch from using Slicer 3D on my MacBook to a newer Windows version to help workflow on a project. However, the Radiomics extension doesn’t now work when you try to install in via the Slicer 3D exten…

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## [Reminder: Last Project Week preparation meeting tomorrow](https://discourse.slicer.org/t/reminder-last-project-week-preparation-meeting-tomorrow/21396)

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**Author:** [@Sam\_Horvath](https://discourse.slicer.org/u/Sam_Horvath)\
**Replies:** 0\
**Last updated:** [January 10, 2022, 9:17pm UTC](https://discourse.slicer.org/t/reminder-last-project-week-preparation-meeting-tomorrow/21396 "2022-01-10T21:17:36Z")

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Dear members of the Project Week community, Please join us for our last Project Week 36 preparation meeting tomorrow January 11 (10 am Boston time, EDT) on Zoom. In this meeting, we will finalize project pages and proj…

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